Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

Very large segmentation errors with recon-all
by Tornabene, Danilo 22 Jul '24

22 Jul '24

External Email - Use Caution Dear FreeSurfer developers, I've encountered very large, systematic errors in segmentation running recon-all on a MRI dataset of 76 subjects. In the screenshot attached, you can see how the white surface (shown in the right hemisphere) includes most of the cortex as well, while the pial surface (in the left hemisphere) extends into the CSF and often reaches the skull. In some of the subjects there is also a clear misalignment with the T1 images. I don't have a long experience with FreeSurfer, but my supervisor Prof. Cole tells me he has processed thousands of scans and never seen this kind of errors so we thought of reaching out to you for some help or explanation. The only thing we noticed is that this error happens on scans with a higher-than-usual resolution (voxels are 0.8x0.8x0.8 mm), could this be causing the problem? I have simply ran recon-all withouth any additional option or argument other than the input files and IDs and the output directory. Please find the shell log outputs for two sample subjects. The recon-all pipeline was completed with no hard errors, and the Euler numbers were mostly 2 with some 1. Best, Danilo Tornabene

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ConcatenateSubregionsResults
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 22 Jul '24

22 Jul '24

External Email - Use Caution Hi Dr. Iglesias, The script ConcatenateSubregionsResults<https://surfer.nmr.mgh.harvard.edu/fswiki/ConcatenateSubregionsResults?acti…>.sh is not readily available, either in the page or the most latest version of FS, could you share? Victor Zeng Beth Israel Deaconess Medical Center PI: Keshavan, Lizano, Bolo -- ---------------------------------------------------------------------- PLEASE NOTE: This message is intended for the use of the person to whom it is addressed. It may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the intended recipient, your use of this message for any purpose is strictly prohibited. If you have received this communication in error, please delete the message and notify the sender so that we may correct our records. See our web page at http://www.bilh.org for a full directory of Beth Israel Lahey Health sites, staff, services and career opportunities.

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Open question to everyone about publicly available MRI datasets
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 18 Jul '24

18 Jul '24

External Email - Use Caution Hi everyone, Does anyone have any leads to publicly available 0.8 x 0.8 x 0.8 mm slice thickness GE structural scans, especially ones outside NDA.nih.gov? This is for a segmentation project. Thank you, Victor Zeng Beth Israel Deaconess Medical Center PI: Keshavan, Lizano, Bolo -- ---------------------------------------------------------------------- PLEASE NOTE: This message is intended for the use of the person to whom it is addressed. It may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the intended recipient, your use of this message for any purpose is strictly prohibited. If you have received this communication in error, please delete the message and notify the sender so that we may correct our records. See our web page at http://www.bilh.org for a full directory of Beth Israel Lahey Health sites, staff, services and career opportunities.

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(no subject)
by 李梦君 17 Jul '24

17 Jul '24

External Email - Use Caution Dear Freesurfer Team I have extracted the left and right cerebral cortex from the aseg.mgz file in the 3d slicer. At the same time, I have loaded the lh.pial and rh.pial in the 3d slicer the left and right cerebral cortex extracted from the aseg.mgz file was not in the same position with the lh.pial and rh.pial in the 3d slicer How should I put them in the same position in the 3d slicer Thanks Mengjun

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BUG: FTP Server data visible without credential
by Kavar Hardik 17 Jul '24

17 Jul '24

External Email - Use Caution Hello FreeSurfer Developers, I am checking your website and I found your FTP server are configured without Credentials. FTP URL: https://surfer.nmr.mgh.harvard.edu/ftp/ POC attached with mail. Regards Kavar Hardik

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Steps for Correcting Dura Using Multi-echo MPRAGE
by KEITH JONES 17 Jul '24

17 Jul '24

External Email - Use Caution Hi everyone, I am running Freesurfer on some multi-echo MPRAGE data in order to extract cortical thickness. I would like to use the multi-echo data to improve the surfaces, and I found example code to do that on a previous post. However, it's not clear to me if there are any steps after this. Do I need to rerun any part of recon-all in order to use these newly created surfaces for cortical parcellation and thickness extraction? My exact code is below: Step 1: Run recon-all recon-all -subject ${SUBJECT} -i {T1RMS} -sd ${OUTPUT} -mprage -3T -T2 ${T2} -T2pial -hires -threads 16 -all Step 2: Adjusting dura mris_make_surfaces -dura memprage_echo%d.mgz 4 -sdir ${OUTPUT} ${SUBJECT} ${HEMI} Step 3: Rerun part of recon-all to use the new surfaces? Step 4: Extract data with aparcstats2table Thanks for the help! Sincerely, Keith Jones

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mri_gtmpvc RBV - cannot find file from a custom subject directory
by Sneha Pandya 17 Jul '24

17 Jul '24

External Email - Use Caution Dear team, I am running mri_gtmpvc using RBV correction, however when I do so I get an error message saying it cannot find $SUBJECTS_DIR/$subject_id/mri/orig.mgz needed for RBV. Our Freesurfer outputs are nested as $subject_id/MPRAGE/Freesurfer/mri/orig.mgz. I tried mri_gtmpvc with "--sd" flag as well, still same error as when I set "--sd $subject_id/MPRAGE/Freesurfer" it tries to find the file as $subject_id/MPRAGE/Freesurfer/$subject_id/mri/orig.mgz. One way I can avoid doing this is by creating a soft link with the expected path, however if there is a better way to do so that would be great. Thank you, Sneha

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Maps from fsLR system (32, 492 vertices) to fsaverage5
by Stefano Delli Pizzi 14 Jul '24

14 Jul '24

External Email - Use Caution Dear, We are using the Magicc Maps (https://github.com/kwagstyl/MAGICC) The maps are in fsLR system (32,492 vertices). How can we register them in fsaverage5? Thanks Best regards Stefano

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Functional connectivity: sig.nii.gz values seem off
by Doll, Laura 12 Jul '24

12 Jul '24

External Email - Use Caution Hi, I ran a functional connectivity analysis according to the walkthrough in the Freesurfer Wiki. After the group analysis (with mri_glmfit using ces and cesvar), I plotted the results (sig.nii.gz of the GLM) with freeview, but the distribution seems off. I'll attach a screenshot, but in case someone cannot access it: There are only few negative data points, the majority seems to be in two (!) approx. gaussian distributions centered at ~5 (the smaller one) and ~8, so most points have values between 5 and 10. Running an FDR correction suggested that the threshold should be 1.3 Because the seems highly unlikely, I search the mailing list archive and found out about the bug in the functional connectivity analysis. Therefore, I repeated the group analysis with the pcc instead of the ces, but that didn't really change anything. Side note/question here: There is no variance corresponding to cesvar I could use in that case, right? Any suggestions on what could've gone wrong? Here are the exact steps I used: # Create nuisance variables for white matter: fcseed-config -wm -fcname wm.dat -fsd bold -pca -cfg wm.config fcseed-sess -sf Part3HR -cfg wm.config # Create nuisance variables for ventricles + CSF: fcseed-config -vcsf -fcname vcsf.dat -fsd bold -pca -cfg vcsf.config fcseed-sess -sf Part3HR -cfg vcsf.config # Auditory cortex ################## # configure parameters fcseed-config -roi AC-rh -fcname AC-rh.dat -fsd bold -mean -cfg AC-rh.config # create FC seeds fcseed-sess -sf Part3HR -cfg AC-rh.config # FC analysis mkanalysis-sess -analysis fc.AC.surf.rh -surface fsaverage rh -fwhm 5 -notask -taskreg AC-rh.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run selxavg3-sess -sf Part3HR -a fc.AC.surf.rh isxconcat-sess -sf Part3HR -analysis fc.AC.surf.rh -o AverageFC_AC -all-contrasts -map pcc mri_glmfit --y ./AverageFC_AC/fc.AC.surf.rh/AC-rh/pcc.nii.gz \ --osgm \ --surface fsaverage rh \ --glmdir ./AverageFC_AC/fc.AC.surf.rh/GLM_AC-rh \ --save-eres \ --nii.gz I'd appreciate any input. Thanks in advance! Best regards, Laura

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Doing math on mgz file
by Aaron Tanenbaum 12 Jul '24

12 Jul '24

External Email - Use Caution Is there an equivalent to fslmaths in freesurfer? Thank you

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